[gmx-users] Lysozyme tutorial-error with moleculetype

delara aghaie d_aghaie at yahoo.com
Sun May 20 08:18:07 CEST 2012

Dear Gromacs Users
I am doing Justin's Lysozyme tutorial. In EM step I got the error with molecule type. (I am using Gromacs, 4.0.5)
It was about Cl and Na. I noticed that because I have selected OPLS forcefield, I should change the name of Cl and Na in my .top file to Na+ and Cl-.
I did this and again when using grompp to create *.tpr file for energy minimization, it says that 

WARNING 1 [file topol.top, line 18272]:
  8 non-matching atom names
  atom names from topol.top will be used
  atom names from 1AKI_solv_ions.gro will be ignored
Should I change the ions name in .gro file also to Cl-? is it only for atom name or also for atom number (coulumn 2 in .gro file)?

Thanks Regards

 From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Wednesday, 16 May 2012, 19:08
Subject: Re: [gmx-users] PMF profile from Umbrella - Plateau

On 5/16/12 10:25 AM, Steven Neumann wrote:
> Dear Justin,
> I pulled my ligad away of 6nm from the protein and obtained beautiful and smooth
> curve of PMF using 28 windows. Starting from zero kcal/mol corresponding to app
> 0.3 nm then minima and curve increase till my plateau which starts from app 1 nm
> - then I have nearly straight line till 6.3 nm.
> My question: Can I decrease pulling distance to save time for the future
> simualtions with this system in terms of number of water molecules? Shall I just
> pull it away of 2-3 nm and I will obtain the same deltaG?

Ideally, one would separate the molecules such that they are no longer interacting.  Obviously with methods like PME this is impossible, so what you're after is sufficient separation such that there is negligible interaction between the protein and ligand.  The required distance depends on the nature and size of the ligand, the types of interactions it experiences, and the cutoffs used. Keep in mind that even if a molecule is beyond the longest nonbonded cutoff, there are still effects like water ordering that can persist up to about 1.0 nm, so I would certainly make sure that all the atoms of the ligand and protein are separated by a minimum of twice the longest cutoff or so to account for this effect.  Note that this would imply the use of g_mindist, not g_dist, as the distance I'm talking about is not the same as the COM distance.

That's just my own rule of thumb for an initial check; you'll have to analyze your own system to decide what's happening and what you should do.


-- ========================================

Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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